4WWF

High-resolution structure of two Ni-bound forms of the M123C mutant of C. metallidurans CnrXs

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	PEG 3350, HEPES, ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.91	α = 90
b = 47.52	β = 90
c = 193.74	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2012-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.98027	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.1	25	98.1	0.083	0.09	16.03	6		156029		-3	11.987

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.16	95.6		0.586	0.689	3.51

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.1	24.79	77363	4038	98.42	0.1164	0.115	0.1448	RANDOM	13.88

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.05			0.03		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.583
r_sphericity_free	29.542
r_dihedral_angle_4_deg	22.655
r_sphericity_bonded	13.904
r_dihedral_angle_3_deg	13.861
r_rigid_bond_restr	4.386
r_dihedral_angle_1_deg	4.225
r_mcangle_it	2.511
r_mcbond_it	2.116
r_mcbond_other	2.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.583
r_sphericity_free	29.542
r_dihedral_angle_4_deg	22.655
r_sphericity_bonded	13.904
r_dihedral_angle_3_deg	13.861
r_rigid_bond_restr	4.386
r_dihedral_angle_1_deg	4.225
r_mcangle_it	2.511
r_mcbond_it	2.116
r_mcbond_other	2.107
r_angle_refined_deg	1.768
r_angle_other_deg	0.871
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1720
Nucleic Acid Atoms
Solvent Atoms	429
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.